PD5117 Sample Summary

## `summarise()` has grouped output by 'patient', 'age_at_sample_exact', 'age_at_sample', 'DOB', 'DATE_OF_DIAGNOSIS'. You can override using the `.groups` argument.
## Joining, by = "PDID"
patient ID age_at_sample_exact cell_type phase BaitLabel
2 PD5117 PD5117d 68.65708 WGS Recapture d
3 PD5117 PD5117e 80.09309 WGS Recapture e
1 PD5117 COLONY82 81.92471 BFU-E-Colony Colony NA

Tree

tree=plot_basic_tree(PD$pdx,label = PD$patient,style="classic")

Expanded Tree with Node Labels

The nodes in this plot can be cross-referenced with nodes specified in subsequent results. The plot also serves to give an idea of what the topology at the top of the tree looks like.

tree=plot_basic_tree(expand_short_branches(PD$pdx,prop = 0.1),label = PD$patient,style="classic")
node_labels(tree)

Timing of driver mutations (using Model = poisson_tree )

Note that the different colours on the tree indicate the separately fitted mutation rate clades.

Driver Specific Mutation Rates & Telomere Lengths by Colony & Timepoint

## 
## Random-Effects Model (k = 1; tau^2 estimator: REML)
## 
##   logLik  deviance       AIC       BIC      AICc 
##   0.0000   -0.0000    4.0000      -Inf   16.0000   
## 
## tau^2 (estimated amount of total heterogeneity): 0
## tau (square root of estimated tau^2 value):      0
## I^2 (total heterogeneity / total variability):   0.00%
## H^2 (total variability / sampling variability):  1.00
## 
## Test for Heterogeneity:
## Q(df = 0) = 0.0000, p-val = 1.0000
## 
## Model Results:
## 
## estimate      se     zval    pval    ci.lb    ci.ub 
##  17.1726  0.3777  45.4682  <.0001  16.4323  17.9128  *** 
## 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'patient'. You can override using the `.groups` argument.
node driver status child_count type colony_count mean_lambda_rescaled correction sd_rescaled lb_rescaled ub_rescaled median_rescaled p_lt_wt
-1 WT 1 -1 local 39 17.17255 1.013181 0.1426444 16.89712 17.45471 17.17156 NA
94 JAK2 1 49 local 49 17.88570 1.013181 0.2606240 17.39160 18.41653 17.87925 0.006225

Driver Acquisition Timeline

All ages are in terms of post conception years. The vertical red lines denote when colonies were sampled and blue lines when targeted follow up samples were taken.

patient node driver child_count lower_median upper_median lower_lb95 lower_ub95 upper_lb95 upper_ub95 N group age_at_diagnosis_pcy max_age_at_sample min_age_at_sample
PD5117 94 JAK2 49 0.0550276 11.50331 0.0315347 0.1186367 9.918325 13.22771 3 JAK2 65.68378 82.65298 69.38535
PD5117 125 TET2 2 25.2104523 42.72000 23.2099085 27.2509644 40.410834 45.00196 3 TET2 65.68378 82.65298 69.38535
PD5117 135 9pUPD 3 20.4197451 46.21496 18.5837464 22.3284887 44.089027 48.25920 3 9pUPD 65.68378 82.65298 69.38535

Copy Number Variation and Timing

Summary of LOH timing inference

## Timings using the Clade Specific Rates
label node het.sensitivity chr start end nhet nhom mean_loh_event lower_loh_event upper_loh_event t_before_end t_before_end_lower t_before_end_upper kb count_in_bin count_se pmut pmut_se xmean xse_mean xsd x2.5. x50. x97.5. xn_eff xRhat lmean lse_mean patient driver3 child_count
9pUPD_A 135 0.9597 9 14690 28231047 0 1 40.55 28.28 46.04 5.654 0.1594 17.92 28200000 5561 74.57 0.012145 0.0001629 0.7806 0.0011827 0.1879 0.30448 0.8325 0.9938 25243 1 5.475 0.0004857 PD5117 9pUPD:JAK2 3
9pUPD_B 46 0.9108 9 14690 28231047 10 2 NA NA NA NA NA NA 28200000 5561 74.57 0.012145 0.0001629 0.2736 0.0007983 0.1218 0.07196 0.2625 0.5373 23271 1 11.104 0.0009423 NA NA NA
9pUPD_C 48 0.8862 9 14690 15677291 2 1 NA NA NA NA NA NA 15600000 2708 52.04 0.005914 0.0001136 0.5168 0.0012623 0.2036 0.11852 0.5260 0.8736 26029 1 7.197 0.0008770 NA NA NA

Duplications?

VAF Distribution of Targeted Follow Up Samples

Here we exclude all local CNAs and depict as color VAF plots